One weekday during morning prayer at R.E. Lee Memorial Church in Lexington, three men walked forward. One announced, “We’ve come to pay homage to General Lee.” I pointed them to the nearby chapel on the Washington and Lee campus, which holds his remains, portrait and statue.

Confederate battle flags, or their replicas, surrounded the statue from 1930 until last week, when the university removed them. To me, their absence pays more homage to the memory of its most famous president than their presence. Judging from the thousands of his letters I’ve read in exploring his faith, for all his deeds, heritage and acclaim (and animosity) accorded him, Robert Edward Lee was at heart a humble soul striving to do his duty to his God and his country. Those flags didn’t fit the person who came to Lexington in 1865.

Soon after surrendering at Appomattox, he encountered an old friend from Mexican War days, Marsena Patrick, then the Union general overseeing provisions for Richmond’s residents. Lee reportedly told Patrick, “the only question on which we did not agree has been settled, and the Lord has decided against me.”

Lee, the soldier, became a man of peace. He had vetoed any notions of waging guerrilla warfare; he counseled Confederate associates to stay in the country and share in rebuilding and reconciling it. And he agreed to lead Washington College because he believed it was his Providential duty—because God wished it.

After the devastated school’s trustees daringly asked Lee to become their president, Lee visited an Episcopal clergy friend who tried to guide him toward larger, more prominent situations. Lee argued instead that “this door and not another was opened to him by Providence,” and he wanted his remaining years to be “a comfort and a blessing to his suffering country.”

Lee came to Lexington on a mission. “I think it is the duty of every citizen, in the present condition of the Country, to do all in his power to aid in the restoration of peace and harmony,” he wrote the trustees. “It is particularly incumbent upon those charged with the instruction of the young to set them an example.”

Countless stories describe him doing just that. At VMI parades, Lee famously marched out of step with cadets because his military days had passed. Several times, he quashed student actions against the Freedmen’s Bureau or African Americans. While he never lamented his Confederate service, he knew that the future lay elsewhere, in a reunited United States. To that cause he gave his last five years.

One old account describes him advising an embittered Confederate widow. “Madam, do not train up your children in hostility to the government of the United States. Remember, we are all one country now. Dismiss from your mind all sectional feeling, and bring them up to be Americans.”

Someone wrote me of a woman asking Lee what to do with an old battle flag. Lee supposedly responded, “Fold it up and put it away.” Though I’ve not verified the account, it is consistent with his letters and acts of his last years. He was always looking ahead.

Of course, his past remained ever with him, as it does today. Edward Valentine’s recumbent statue depicts Lee asleep, on a battlefield, in a Confederate general’s uniform. He served a cause that promoted secession and slavery even though he personally opposed both. Such are the paradoxes of history: The university’s other namesake, George Washington, owned vastly more slaves than Lee ever did (which were few if any). Lincoln’s assessment of people of color was as ill-informed as Lee’s or most other whites of that era.

Museums are designed to help us ponder such paradoxes. But Lee did not build the chapel as a museum, much less a shrine to the Lost Cause. He meant it to be a gathering place for the college — and wider community — in prayer, in learning, and in celebration. Daily prayers aren’t offered as when Lee was president, but the learning, the celebration, and sometimes the prayers, abide.

The university has folded up replicas, placed in 1995, of battle flags that appeared only in 1930. Working with the American Civil War Museum, it will bring real flags to serve educational purposes in the museum in the chapel’s crypt.

Meanwhile, the “Lee chamber” now looks as it did in 1883, as his family then intended, to remember a soldier who became an advocate and exemplar of peace.